 command executed: rosetta.gcc -s 1ubq.pdb -idealize -fa_input 
 [T/F  OPT]Default FALSE value for [-version]
 [T/F  OPT]Default FALSE value for [-score]
 [T/F  OPT]New TRUE value for [-idealize]
 [T/F  OPT]Default FALSE value for [-local]
 Rosetta mode: idealize  
 [T/F  OPT]Default FALSE value for [-chain]
 [T/F  OPT]Default FALSE value for [-protein]
 [T/F  OPT]Default FALSE value for [-series]
 [INT  OPT]Default value for [-nstruct]  1
 [T/F  OPT]Default FALSE value for [-read_all_chains]
 [T/F  OPT]Default FALSE value for [-no_filters]
 [T/F  OPT]Default FALSE value for [-scorefxn]
 default centroid scorefxn:  4
 default fullatom scorefxn:  12
 [T/F  OPT]New TRUE value for [-fa_input]
 [T/F  OPT]Default FALSE value for [-repack]
 [STR  OPT]Default value for [-atom_vdw_set] default.
 [STR  OPT]Default value for [-fa_lj_rep_slope] highres.
 [T/F  OPT]Default FALSE value for [-silent_input]
 [T/F  OPT]Default FALSE value for [-status]
 [T/F  OPT]Default FALSE value for [-output_all]
 [STR  OPT]Default value for [-cst] cst.
 [STR  OPT]Default value for [-dpl] dpl.
 [T/F  OPT]Default FALSE value for [-chain_inc]
 [T/F  OPT]Default FALSE value for [-ssblocks]
 [T/F  OPT]Default FALSE value for [-find_disulf]
 [T/F  OPT]Default FALSE value for [-fix_disulf]
 [T/F  OPT]Default FALSE value for [-ex1]
 [T/F  OPT]Default FALSE value for [-ex2]
 [T/F  OPT]Default FALSE value for [-ex3]
 [T/F  OPT]Default FALSE value for [-ex34]
 [T/F  OPT]Default FALSE value for [-usenatchi]
 [T/F  OPT]Default FALSE value for [-ex1aro]
 [T/F  OPT]Default FALSE value for [-ex2aro_only]
 [INT  OPT]Default value for [-extrachi_cutoff]  18
 [T/F  OPT]Default FALSE value for [-movie]
 [T/F  OPT]Default FALSE value for [-trajectory]
 [STR  OPT]Default value for [-moviefile] -.
 [STR  OPT]Default value for [-scorefile] -.
 [INT  OPT]Default value for [-run_level]  0
 [T/F  OPT]Default FALSE value for [-silent]
 [T/F  OPT]Default FALSE value for [-verbose]
 [T/F  OPT]Default FALSE value for [-gush]
 [T/F  OPT]Default FALSE value for [-yap]
 [T/F  OPT]Default FALSE value for [-chat]
 [T/F  OPT]Default FALSE value for [-inform]
 [T/F  OPT]Default FALSE value for [-quiet]
 run level:  0
 [T/F  OPT]Default FALSE value for [-benchmark]
 [T/F  OPT]Default FALSE value for [-debug]
 [STR  OPT]New value for [-s] 1ubq.pdb.
 Starting structure: 1ubq
 [STR  OPT]Default value for [-paths] paths.txt.
 [T/F  OPT]Default FALSE value for [-constant_seed]
 # =====================================
 # random seed number is  1614261
 # =====================================
 Reading ../rosetta_database/Rama_smooth_dyn.dat_ss_6.4 
 Reading ../rosetta_database/phi.theta.36.HS.resmooth 
 Reading ../rosetta_database/phi.theta.36.SS.resmooth 
 Reading ../rosetta_database/template.pdb 
 Atom_mode set to polH&aroH 
 reading starting structure: ./1ubq.pdb
    
 clean_pdb: fill missing atoms, optimize H positions
 initializing full atom subroutines
 Reading ../rosetta_database/bbind00.Nov.lib 
 Reading ../rosetta_database/DunbrackBBDepRots12.dat 
 Reading ../rosetta_database/dunsd 
 Finished reading Dunbrack parameters
 Reading ../rosetta_database/pdbpairstats_fine 
 Reading ../rosetta_database/sc_hbW 
 Reading ../rosetta_database/Paa 
 Reading ../rosetta_database/Paa_n 
 Reading ../rosetta_database/paircutoffs 
 Reading ../rosetta_database/Paa_pp 
 generating Etable...
 Starting energy table calculation
 Energy table parameter set: allh       Revision: 1.8 Date: 2002/07/05 23:53:23
 Finished calculating energy tables.
 Reading ../rosetta_database/avgE_from_pdb 
 done initalizing full atom subroutines
 Done initializing full atom routines
 Filling missing atoms
 creating preliminary hbond arrays
 optimizing missing atoms
 optimizing hydrogen positions
 end of clean_pdb
  
 WARNING:: end of pdb file reached: angle, secstruct, & res info not found
 Looking for dssp file:./1ubq.dssp 
 Warning!! dssp file not found
 Looking for secondary structure assignment file:./1ubq.ssa 
 Warning!! ssa file not found
 calculating secondary structure from torsion angles
 [T/F  OPT]Default FALSE value for [-regions]
 Reading ../rosetta_database/SASA-masks.dat 
 Reading ../rosetta_database/SASA-angles.dat 
 ========================================
 OUTPUT PDB: ./1ubq_idl.pdb 
 NEXT STRUCTURE: ./1ubq_idl.pdb 
 initializing full atom coordinates
 idealizing residues  1 to  76
  Initializing refold
 minimization
 window weight vomega iter   fret      rms       rama      ljrep     ljatr    tether    omega    phipsi
 ------ ------ ------ ---- --------- -------- --------- --------- --------- --------- --------- ---------
    76  1.000   T      0    8261.14     4.089    20.288  3620.135  -346.354  4985.325     0.000     0.000
    60  1.000   F     63    -265.94     0.381    20.026    25.782  -316.569    21.763     0.000     5.390
    76  0.001   T     68      12.31     0.257    19.251    21.035  -306.994     8.001     1.716     4.800
    76  1.000   T     27    -292.96     0.350    20.403     6.836  -317.256    11.968     2.542     4.714
 rms to starting angles  1.98433447
 root mean dme to starting coordinates  0.184237823
 global ca_rms to starting coordinates  0.349919587
 ======================================================
DONE ::     1 starting structures built     1 (nstruct) times
This process generated     1 decoys from      1 attempts
                           0 starting pdbs were skipped
 ======================================================
